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Primer on Reading Frames and Phase Wilson Leung08/2012.

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Presentation on theme: "Primer on Reading Frames and Phase Wilson Leung08/2012."— Presentation transcript:

1 Primer on Reading Frames and Phase Wilson Leung08/2012

2 3 reading frames per strand (+ / -) Frame: base to start translation relative to the first base of the sequence 1: Start translation at first base of sequence 2: Start translation at second base of sequence 3: Start translation at third base of sequence A genomic sequence has 6 reading frames 1 2 3 Frames

3 Splice donor and acceptor phases Phase: Number of bases between the complete codon and splice site – Donor phase: Number of bases between the end of last complete codon and the splice donor site (GT/GC) – Acceptor phase: Number of bases between splice acceptor site (AG) and the start of first complete codon Phase is relative to the reading frame of the exon

4 Phase depends on the reading frame Acceptor phase: – Phase 2 relative to frame 1 – Phase 0 relative to frame 2 – Phase 1 relative to frame 3 Splice acceptor

5 Compatibility of donor and acceptor site Donor and acceptor phases of adjacent exons must be compatible with each other: ( (Donor phase + Acceptor phase) % 3 ) == 0 GTAG… … … CC A AA T G CT C GA T TT P P N N V V L L D D Translation: CC A AA T G CT C GA T GTT CC A AA T CT C GA T TT

6 Incompatible donor and acceptor phases introduce a frame shift in the translation CC A GTAG… AA T G CT C GA T TT P P N N G G F F S S Translation: GT CC A AA T TC G ATGGTGGT TTC Phase 0 donor and phase 2 acceptor are incompatible with each other

7 Calculating the exon acceptor phase where: i > 1 P i = Acceptor phase of exon i L i-1 = Length of previous exon P i-1 = Acceptor phase of previous exon L i-1 - P i-1 =Previous exon length starting from the first complete codon (L i-1 - P i-1 ) % 3=Donor phase of previous exon 3 - ((L i-1 - P i-1 ) % 3)=Acceptor phase of current exon (3 - ((L i-1 - P i-1 ) % 3 )) % 3=Change to phase 0 if acceptor phase is 3

8 Questions? http://www.flickr.com/photos/wingedwolf/5471047557/sizes/m/in/photostream/


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